BMS 631: Lecture 3 - Purdue University

BMS 631: Lecture 3 - Purdue University

BMS 631: Lecture 4 Fluorescence J. Paul Robinson, PhD SVM Professor of Cytomics & Professor of Biomedical Engineering Purdue University www.cyto.purdue.edu Notice: The materials in this presentation are copyrighted materials. If you want to use any of these slides, you may do so if you credit each slide with the authors name. It is illegal to place these notes on CourseHero. All materials used in this course are available for download on the web at http://tinyurl.com/2wkpp 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Slide 1 Last updated Feb, 2012

Absorption Basic quantum mechanics requires that molecules absorb energy as quanta (photons) based upon a criteria specific for each molecular structure Absorption of a photon raises the molecule from ground state to an excited state Total energy is the sum of all components (electronic, vibrational, rotational, translations, spin orientation energies) (vibrational energies are quite small) The structure of the molecule dictates the likely-hood of absorption of energy to raise the energy state to an excited one 3rd Ed Shapiro p 84 Slide 2 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Lifetime Absorption associated with electronic transitions (electrons changing states) occurs in about 1

femtosecond (10-15 s) The lifetime of a molecule depends on how the molecule disposes of the extra energy but many fluorophores have lifetimes around 5 ns Because of the uncertainty principle, the more rapidly the energy is changing, the less precisely we can define the energy So, long-lifetime-excited-states have narrow absorption peaks, and short-lifetime-excited-states have broad absorption peaks 3rd Ed. Shapiro p 85 4th Ed. Shapiro p 110 Slide 3 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Extinction Using Beers law (Beer-Lambert law) for light travelling through a curvette thickness d cm containing n molecules/cm3 ln (Io/I) = nd where Io and I are the light entering and leaving and is the molecular property

called the absorption cross section Now we can state that ln (Io/I) = Cd where C is the concentration and a is the absorption coefficient which reflects the capacity of the absorbing substance to absorb light If there are n (molecules/cm3 ; d in cm, must be in cm2 so if is in cm2/ mol, C must be in mol/cm3 do C=a/103 giving log10 (Io/I) = d = A where A is the absorbance or optical density and is the decadic molar exctinction coeficient in dm3mol-1cm-1 3rd Ed. Shapiro p 86 4th Ed. Shapiro p 111 Slide 4 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Absorbance O.D. units or absorbance is expressed in logarithmic terms

so they are additive. e.g. an object of O.D. of 1.0 absorbs 90% of the light. Another object of O.D. 1.0 placed in the path of the 10% of the light 10% of this light or 1% of the original light is transmitted by the second object It is possible to express the absorbance of a mixture of substances at a particular wavelength as the sum of the absorbances of the components You can calculate the cross sectional area of a molecule to determine how efficient it will absorb photons. The extinction coefficient indicates this value 3rd ed. Shapiro p 87 4th Ed. Shapiro p 111 Slide 5 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Parameters Extinction Coefficient

refers to a single wavelength (usually the absorption maximum) the cross sectional area of a molecule determines how efficient it will absorb photons Quantum Yield Qf is a measure of the integrated photon emission over the fluorophore spectral band At sub-saturation excitation rates, fluorescence intensity is proportional to the product of and Qf Slide 6 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence Quantum Yield Q=

photons emitted = photons absorbed kr kr + knr Fluorescence Lifetime ( - is the time delay between the absorbance and the emission = 1 kr + knr R - reactant molecules) 12:54 AM

1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Slide 7 Fluorescence Photon emission as an electron returns from an excited state to ground state Slide 8 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence Excitation Spectrum Intensity of emission as a function of exciting wavelength (this is the absorbance component) Chromophores are components of molecules which absorb light

They are frequently aromatic rings Slide 9 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence The wavelength of absorption is related to the size of the chromophores Smaller chromophores, higher energy (shorter wavelength) Slide 10 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Electromagnetic Spectrum Microsoft Corp, 1995

Only a very small region within the ES is used for flow cytometry applications Slide 11 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Properties of Fluorescent Molecules Large extinction coefficient at the region of excitation High quantum yield Optimal excitation wavelength

Photostability Excited-state lifetime Minimal perturbation by probe Slide 12 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Simplified Jablonski Diagram S 1 Energy S1 hvex hvem

S0 Slide 13 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence Jablonski Diagram Singlet States Triplet States Vibrational energy levels Rotational energy levels Electronic energy levels ENERGY S2 S1

IsC ABS FL I.C. T2 T1 PH IsC S0 [Vibrational sublevels] 3rd Ed. Shapiro p 87 4th Ed. Shapiro p 112 ABS - Absorbance

S 0.1.2 - Singlet Electronic Energy Levels FL - Fluorescence T 1,2 - Corresponding Triplet States I.C.- Nonradiative Internal Conversion IsC - Intersystem Crossing PH - Phosphorescence Slide 14 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence Stokes Shift Fluorescnece Intensity is the energy difference between the lowest energy peak of absorbance and the highest energy of emission Fluorescein molecule

Stokes Shift is 20 + nm 495 nm 518 nm Wavelength 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Slide 15 Fluorescence The longer the wavelength the lower the energy The shorter the wavelength the higher the energy eg. UV light from sun - this causes the sunburn, not the red visible light

Slide 16 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence Excitation Spectra Intensity related to the probability of the event Wavelength the energy of the light absorbed or emitted Slide 17 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Conclusions Dye molecules must be close to but below saturation levels for optimum

emission Fluorescence emission is longer than the exciting wavelength The energy of the light increases with reduction of wavelength Slide 18 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Relative absorbance of phycobiliproteins Phycobiliproteins are stable and highly soluble proteins derived from cyanobacteria and eukaryotic algae with quantum yields up to 0.98 and molar extinction coefficients of up to 2.4 10 6 (ABS=Absorbance) Protein 488nm % ABS 568nm % ABS

633nm % ABS B-phycoerytherin 33 97 0 R-phycoerytherin 63 92 0 allophycocyanin

0.5 20 56 Data from Molecular Probes Website Slide 19 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Allophycocyanin (APC) Protein 300 nm 400 nm 500 nm 632.5 nm (HeNe)

600 nm 700 nm Excitation Emission Slide 20 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Some Common Laser lines 350 300 nm 457 488 514 400 nm 500 nm

Common Laser Lines 610 632 600 nm 700 nm PE-TR Conj. Texas Red PI Ethidium PE FITC 325nm cis-Parinaric acid Slide 21 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt

Quenching, Bleaching & Saturation Quenching is when excited molecules relax to ground states via nonradiative pathways avoiding fluorescence emission (vibration, collision, intersystem crossing) Molecular oxygen quenches by increasing the probability of intersystem crossing Polar solvents such as water generally quench fluorescence by orienting around the exited state dipoles 3rd Ed. Shapiro p 90 4th Ed. Shapiro p 115 Slide 22 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Photobleaching Defined as the irreversible destruction of an

excited fluorophore Photobleaching is not a big problem for flow cytometry as long as the time window for excitation is very short (a few hundred microsconds) Slide 23 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Photobleaching example from microscopy FITC - at 4.4 x 1023 photons cm-2 sec-1 FITC bleaches with a quantum efficiency Qb of 3 x 10-5 Therefore FITC would be bleaching with a rate constant of 4.2 x 103 sec-1 so 37% of the molecules would remain after 240 sec of irradiation. In a single plane, 16 scans would cause 6-50% bleaching Slide 24

12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Excitation Saturation The rate of emission is dependent upon the time the molecule remains within the excitation state (the excited state lifetime f) Optical saturation occurs when the rate of excitation exceeds the reciprocal of f In a scanned image of 512 x 768 pixels (400,000 pixels) if scanned in 1 second requires a dwell time per pixel of 2 x 10 -6 sec. Molecules that remain in the excitation beam for extended periods have higher probability of interstate crossings and thus phosphorescence Usually, increasing dye concentration can be the most effective means of increasing signal when energy is not the limiting factor (i.e. laser based confocal systems) Slide 25 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt

Phosphorescence Following absorption, molecules can relax via a nonradiative transition to the T1 rather than the S1 state - this is called an intersystem crossing While it is forbidden it does happen and has a low probability and takes a longer time - the energy dissipated is called phosphorescence Phosphorescence has a longer lifetime than fluorescence (milliseconds rather than femtoseconds Phosphorescence generally occurs at longer wavelengths than fluorescence because the energy difference between S0 and T1 is lower 3rd Ed Shapiro p 88 4th Ed. Shapiro p 113 Slide 26 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Excitation - Emission Peaks Fluorophore

FITC Bodipy Tetra-M-Rho L-Rhodamine Texas Red CY5 EXpeak EM peak % Max Excitation at 488 568 647 nm 496 503 554 572 592 649 518 511 576 590

610 666 87 58 10 5 3 1 0 1 61 92 45 11 0 1 0 0 1

98 Note: You will not be able to see CY5 fluorescence under the regular fluorescent microscope because the wavelength is too high. Slide 27 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Resonance Energy Transfer Resonance energy transfer can occur when the donor and acceptor molecules are less than 100 of one another (preferable 20-50 ) Energy transfer is non-radiative which means the donor is not emitting a photon which is absorbed by the acceptor Fluorescence RET (FRET) can be used to spectrally shift the fluorescence emission of a molecular combination. 3rd Ed. Shapiro p 90

4th Ed. Shapiro p 115 Slide 28 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt FRET properties Isolated donor Donor distance too great Donor distance correct Slide 29 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence Resonance Energy Transfer Molecule 1 Molecule 2 Fluorescence

Intensity Fluorescence ACCEPTOR DONOR Absorbance Absorbance Wavelength Slide 30 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Note added of interest First synthesis of fluorescein: A. Von Baeyer, Ber Deutch Chem Ges 4:555. 1871 Recent uses of fluorescent protein molecules FUCCI

Fluorescent Ubiqutination based cell cycle Indicator (fluorescent protein-based system that employs both a red (RFP) and a green (GFP) fluorescent protein fused to different regulators of the cell cycle: cdt1 and geminin. ) From Invitrogen website: Developed by Miyawaki and colleagues1, the fluorescence ubiquitination cell cycle indicator (FUCCI), is a genetically encoded, two-color (red and green), indicator that lets you follow cell division within a cell population. We have incorporated the FUCCI genetic constructs into the powerful BacMam gene delivery system, creating a simple and efficient method for labeling cells and following their division: Population-level, real-time cell cycle phase determination Easy and efficient labeling through BacMam gene delivery system http://cell.firstlightera.com/EN/Microsites/1/Invitrogen/PremoFUCCI Slide 31 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Raman Scatter A molecule may undergo a vibrational transition (not an electronic shift) at exactly the same time as scattering occurs This results in a photon emission of a photon

differing in energy from the energy of the incident photon by the amount of the above energy - this is Raman scattering. The dominant effect in flow cytometry is the stretch of the O-H bonds of water. At 488 nm excitation this would give emission at 575-595 nm 3rd Ed. Shapiro p 93 4th Ed. Shapiro p 118 Slide 32 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Probes for Proteins Probe Excitation FITC 488 525 PE 488 575 APC 630 650

PerCP 488 680 Cascade Blue 360 Coumerin-phalloidin 350 Texas Red 610 630 Emission 450 450 Tetramethylrhodamine-amines CY3 (indotrimethinecyanines) 540 CY5 (indopentamethinecyanines) 550 575 640 575

670 Slide 33 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Specific Organelle Probes Probe Site BODIPY NBD DPH TMA-DPH Rhodamine 123 DiO diI-Cn-(5) diO-Cn-(3) Excitation

Golgi Golgi Lipid Lipid 505 488 350 350 Mitochondria 488 Lipid 488 Lipid 550 Lipid 488 Emission 511 525

420 420 525 500 565 500 BODIPY - borate-dipyrromethene complexes NBD - nitrobenzoxadiazole DPH - diphenylhexatriene TMA - trimethylammonium Slide 34 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence Overlap Fluorescence Intensity Fluorescein

molecule 488 nm 450 500 550 PE molecule 575 nm 600 650 Wavelength (nm) Overlap of FITC fluorescence in PE PMT Overlap of PE fluorescence in FITC PMT

Slide 35 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Fluorescence The longer the wavelength the lower the energy The shorter the wavelength the higher the energy eg. UV light from sun - this causes the sunburn, not the red visible light The spectrum is independent of precise excitation line but the intensity of emission is not Slide 36 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Mixing fluorochromes When there are two molecules with different absorption spectra, it is important to consider where a fixed wavelength excitation should be placed. It is possible to

increase or decrease the sensitivity of one molecule or another. Slide 37 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Mixing fluorochromes When there are two molecules with different absorption spectra, it is important to consider where a fixed wavelength excitation should be placed. It is possible to increase or decrease the sensitivity of one molecule or another. Slide 38 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Mixing fluorochromes When there are two molecules with different absorption

spectra, it is important to consider where a fixed wavelength excitation should be placed. It is possible to increase or decrease the sensitivity of one molecule or another. Slide 39 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Excitation of 3 Dyes with emission spectra J. Paul Robinson, Class lecture notes, BMS 631 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Slide 40 Change of Excitation J. Paul Robinson, Class lecture notes, BMS 631

12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Slide 41 Slide 42 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt Lecture Summary Light and Matter Absorption Fluorescence From this lecture you should understand:

The nature of fluorescence molecules How fluorescence is generated Why molecules have different excitation and emission What Resonance Energy Transfer is What quantum yield is What fluorescence overlap is How excitation wavelength impacts emission Slide 43 12:54 AM 1990-2012 J. Paul Robinson, Purdue University Lecture0004.ppt

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